Design of peptides interfering with iron-dependent regulator (IdeR) and evaluation of Mycobacterium tuberculosis growth inhibition

Document Type : Original Article


1 Department of Microbiology and Virology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran

2 Antimicrobial Resistance Research Center, Avicenna Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran

3 Tuberculosis Reference Center, Dr Shariati Hospital, Mashhad University of Medical Sciences, Mashhad, Iran

4 Department of Laboratory Sciences, School of Paramedical Sciences, Mashhad University of Medical Sciences, Mashhad


Objective(s): Tuberculosis (TB), a disease caused by Mycobacterium tuberculosis (Mtb), stayed a global health thread with high mortality rate. Since TB has a long-term treatment, it leads high risk of drug resistant development, and there is an urgent to find new drugs. The aim of this study was designing new inhibitors for a new drug target, iron dependent regulator, IdeR.
Materials and Methods: Based on the interaction most populated amino acids of IdeR to the related gene operators, 50 short peptides were modeled. Bonding affinity of short peptides toward DNA were studied by docking. Top 10 best predicted bonding affinity were selected. DNA binding assay, microplate alamar blue assay, colony counting, quantitative real time- PCR (qRT-PCR) of IdeR corresponding genes, cell wall-associated mycobactin and whole-cell iron estimation were done to prove the predicted mechanism of in silico potent constructs.
Results: Amongst the 10 synthesized short peptide candidates, glycine-valine-proline-glycine (GVPG) and arginine-proline-arginine (RPR) inhibited Mtb in vitro at 200 µM concentration. qRT-PCR showed mbtB 58-fold over expression that resulted in Mtb growth inhibition. Cell wall-associated mycobactin and whole-cell iron estimation confirmed the results of qRT-PCR.
Conclusion: We introduced two new lead compounds to inhibit Mtb that are promising for the development of more potent anti-tubercular therapies.


1. World Health Organization (WHO). Global Tuberculo-sis Report. 2015. Available at: http:// www.who. int/tb/ publications/global_report/en/).
2. Matsumoto M, Hashizume H, Tomishige T, Kawasaki M, Tsubouchi H, Sasaki H, et al. OPC-67683, a nitro-dihydro-imidazooxazole derivative with promising action against tuberculosis in vitro and in mice. PLoS Med 2006; 3:e466.
3. Cole ST, Alzari PM. Microbiology. TB- a new target, a new drug. Science 2005; 307:214–215.
4. Chung BK-S, Dick T, Lee D-Y. In silico analyses for the discovery of tuberculosis drug targets. J Antimicrob Chemother 2013; 68:2701–2709.
5. Rodriguez GM, Voskuil MI, Gold B, Schoolnik GK, Smith I. ideR , an essential gene in mycobacterium tuberculosis : role of ideR in iron-dependent gene expression , iron metabolism , and oxidative stress response. Infect Immunol 2002; 70:3371–3381.
6. Pandey R, Rodriguez GM. IdeR is required for iron homeostasis and virulence in Mycobacterium tuberculosis. Mol Microbiol 2014; 91:98–109.
7. Keyer K, Imlay JA. Superoxide accelerates DNA damage by elevating free-iron levels. Proc Natl Acad Sci U S A 1996; 93:13635–13640.
8. Wisedchaisri G, Chou CJ, Wu M, Roach C, Rice AE, Holmes RK. Crystal structures , metal activation, and DNA-Binding properties of two-domain ideR from Mycobacterium tuberculosis. Biochemistry 2007; 46:436–447.
9. El-Ayaan U, Abdel-Aziz AA, Al-Shihry S. Solvatochromism, DNA binding, antitumor activity and molecular modeling study of mixed-ligand copper(II) complexes containing the bulky ligand: Bis[N-(p tolyl)imino]acenaphthene. Eur J Med Chem 2007; 42:1325–1233.
10. Mcalpine B. A colorimetric microassay for the detection of agents that interact with DNA. 1992; 55: 1582–1587.
11. Bronstein JC, Weber PC. A Colorimetric Assay for high-throughput screening of inhibitors of herpes simplex virus Type 1 alkaline nuclease. Anal Biochem [Internet] 2001; 293:239–245.
12. Franzblau SG, Witzig RS, McLaughlin JC, Torres P, Madico G, Hernandez A, et al. Rapid, low-technology MIC determination with clinical Mycobacterium tuberculosis  isolates by using the microplate Alamar Blue assay. J Clin Microbiol 1998; 36:362–366.
13. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 2001; 25:402–408.
14. Schwyn B, Neilands JB. Universal chemical assay for the detection and determination of siderophores. Anal Biochem 1987; 160:47–56.
15. Dragset MS, Poce G, Alfonso S, Padilla-Benavides T, Ioerger TR, Kaneko T, et al. A novel antimycobacterial compound acts as an intracellular iron chelator. Antimicrob Agents Chemother 2015; 59:2256–2264.
16. Ghosh S, Prasad KVS, Vishveshwara S, Chandra N. Rule-based modelling of iron homeostasis in tuberculosis. Mol Biosyst 2011; 7:2750–2768.
17. Hao G, Rongji D, Kui Q, Zhongqiu T, Heyao W. A synthetic peptide derived from NK-lysin with activity against mycobacterium tuberculosis and its structure-function relationship. Int J Pept Res Ther 2011; 17:301–306.
18. Flexner C. HIV drug development: the next 25 years. Nat Rev Drug Discov 2007; 6:959–966.
19. Lau QY, Choo XY, Lim ZX, Kong XN, Ng FM, Ang MJY, et al. A head-to-head comparison of the antimicrobial activities of 30 ultra-short antimicrobial peptides against staphylococcus aureus, pseudomonas aeruginosa and Candida albicans. Int J Pept Res Ther 2015; 21:21–28.v